Journal of Microbiology

Reviews

Microbiome-Mucosal Immunity Nexus: Driving Forces in Respiratory Disease Progression.: Young Chae Park, Soo Yeon Choi, Yunah Cha, Hyeong Won Yoon, Young Min Son; J. Microbiol. 2024;62(9):709-725. Published online September 6, 2024; DOI: https://doi.org/10.1007/s12275-024-00167-4

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Abstract: The importance of the complex interplay between the microbiome and mucosal immunity, particularly within the respiratory tract, has gained significant attention due to its potential implications for the severity and progression of lung diseases. Therefore, this review summarizes the specific interactions through which the respiratory tract-specific microbiome influences mucosal immunity and ultimately impacts respiratory health. Furthermore, we discuss how the microbiome affects mucosal immunity, considering tissue-specific variations, and its capacity in respiratory diseases containing asthma, chronic obstructive pulmonary disease, and lung cancer. Additionally, we investigate the external factors which affect the relationship between respiratory microbiome and mucosal immune responses. By exploring these intricate interactions, this review provides valuable insights into the potential for microbiome-based interventions to modulate mucosal immunity and alleviate the severity of respiratory diseases.

Application of Microbiome‑Based Therapies in Chronic Respiratory Diseases: Se Hee Lee, Jang Ho Lee, Sei Won Lee; J. Microbiol. 2024;62(3):201-216. Published online April 18, 2024; DOI: https://doi.org/10.1007/s12275-024-00124-1

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Abstract: The application of microbiome-based therapies in various areas of human disease has recently increased. In chronic respiratory disease, microbiome-based clinical applications are considered compelling options due to the limitations of current treatments. The lung microbiome is ecologically dynamic and afected by various conditions, and dysbiosis is associated with disease severity, exacerbation, and phenotype as well as with chronic respiratory disease endotype. However, it is not easy to directly modulate the lung microbiome. Additionally, studies have shown that chronic respiratory diseases can be improved by modulating gut microbiome and administrating metabolites. Although the composition, diversity, and abundance of the microbiome between the gut and lung are considerably diferent, modulation of the gut microbiome could improve lung dysbiosis. The gut microbiome infuences that of the lung via bacterial-derived components and metabolic degradation products, including short-chain fatty acids. This phenomenon might be associated with the cross-talk between the gut microbiome and lung, called gut-lung axis. There are multiple alternatives to modulate the gut microbiome, such as prebiotics, probiotics, and postbiotics ingestion and fecal material transplantation. Several studies have shown that high-fber diets, for example, present benefcial efects through the production of short-chain fatty acids. Additionally, genetically modifed probiotics to secrete some benefcial molecules might also be utilized to treat chronic respiratory diseases. Further studies on microbial modulation to regulate immunity and potentiate conventional pharmacotherapy will improve microbiome modulation techniques, which will develop as a new therapeutic area in chronic respiratory diseases.

Journal Articles

Fresh Washed Microbiota Transplantation Alters Gut Microbiota Metabolites to Ameliorate Sleeping Disorder Symptom of Autistic Children: Nai-Hua Liu , Hong-Qian Liu , Jia-Yi Zheng , Meng-Lu Zhu , Li-Hao Wu , Hua-Feng Pan , Xing-Xiang He; J. Microbiol. 2023;61(8):741-753. Published online September 4, 2023; DOI: https://doi.org/10.1007/s12275-023-00069-x

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Abstract: Accumulating studies have raised concerns about gut dysbiosis associating autism spectrum disorder (ASD) and its related symptoms. However, the effect of gut microbiota modification on the Chinese ASD population and its underlying mechanism were still elusive. Herein, we enrolled 24 ASD children to perform the first course of fresh washed microbiota transplantation (WMT), 18 patients decided to participate the second course, 13 of which stayed to participate the third course, and there were 8 patients at the fourth course. Then we evaluated the effects of fresh WMT on these patients and their related symptoms. Our results found that the sleeping disorder symptom was positively interrelated to ASD, fresh WMT significantly alleviated ASD and its sleeping disorder and constipation symptoms. In addition, WMT stably and continuously downregulated Bacteroides/ Flavonifractor/Parasutterella while upregulated Prevotella_9 to decrease toxic metabolic production and improve detoxification by regulating glycolysis/myo-inositol/D-glucuronide/D-glucarate degradation, L-1,2-propanediol degradation, fatty acid β-oxidation. Thus, our results suggested that fresh WMT moderated gut microbiome to improve the behavioral and sleeping disorder symptoms of ASD via decrease toxic metabolic production and improve detoxification. Which thus provides a promising gut ecological strategy for ASD children and its related symptoms treatments.

Relationship Between Mycotoxin Production and Gene Expression in Fusarium graminearum Species Complex Strains Under Various Environmental Conditions: Wenwen Huang , Ping Zhou , Guanghui Shen , Tao Gao , Xin Liu , Jianrong Shi , Jianhong Xu , Jianbo Qiu; J. Microbiol. 2023;61(5):525-542. Published online May 2, 2023; DOI: https://doi.org/10.1007/s12275-023-00046-4

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Abstract: The Fusarium graminearum species complex (FGSC) can produce various mycotoxins and is a major concern for food quantity and quality worldwide. In this study, we determined the effects of water activity ( aw), temperature, incubation time and their interactions on mycotoxin accumulation and the expression levels of biosynthetic genes in FGSC strains from maize samples in China. The highest deoxynivalenol (DON), 3-acetyldeoxynivalenol(3ADON) and 15-acetyldeoxynivalenol (15ADON) levels of the F. boothii and F. graminearum strains were observed at 0.98 aw/ 30 °C or 0.99 aw/ 25 °C. F. asiaticum and F. meridionale reached maximum nivalenol (NIV) and 4-acetylnivalenol (4ANIV) contents at 0.99 aw and 30 °C. With the extension of the incubation time, the concentrations of DON and NIV gradually increased, while those of their derivatives decreased. F. boothii, F. meridionale and one F. asiaticum strain had the highest zearalenone (ZEN) values at 0.95 aw and 25 °C, while the optimum conditions for the other F. asiaticum strain and F. graminearum were 0.99 aw and 30 °C. Four genes associated with trichothecene and zearalenone synthesis were significantly induced under higher water stress in the early stage of production. The results indicated independence of mycotoxin production and gene expression, as maximum amounts of these toxic metabolites were observed at higher aw in most cases. This study provides useful information for the monitoring and prevention of such toxins entering the maize production chain.

Detection of colistin-resistant populations prior to antibiotic exposure in KPC-2-producing Klebsiella pneumoniae clinical isolates: Jungyu Seo , Yu Mi Wi , Jong Min Kim , Yae-Jean Kim , Kwan Soo Ko; J. Microbiol. 2021;59(6):590-597. Published online March 29, 2021; DOI: https://doi.org/10.1007/s12275-021-0610-1

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Abstract: Although colistin is frequently regarded as the antibiotic of last resort in treating carbapenem-resistant Klebsiella pneumoniae, colistin heteroresistance may in part be associated with antibiotic treatment failure. However, we do not know how widespread the colistin heteroresistance is in carbapenem- resistant K. pneumoniae isolates. In this study, we performed colistin disc diffusion assays, E-tests, and population analysis profiling for KPC-2-producing K. pneumoniae isolates to identify colistin heteroresistance. Although no colistin- resistant colonies were detected by the disc diffusion test and E-test, a colistin-resistant subpopulation was identified in population analysis profiling in all colistin-susceptible, KPC-2-producing K. pneumoniae isolates. Colistin-resistant subpopulations were also identified even when isolates had no colistin exposure. The ratio of colistin-resistant subpopulations to the total population increased as the exposure concentration of colistin increased. In in vitro time-kill assays, regrowth was observed in all isolates after 2 h upon exposure to colistin. We identified common amino acid alterations in PhoQ, PhoP, and PmrB in colistin-resistant subpopulations from some isolates, but no substitutions were found in most resistant subpopulations from other isolates. In all colistin-resistant subpopulations, overexpression of PhoQ and PbgP was observed. In this study, we demonstrated that colistin heteroresistance may be common in KPC-2-producing K. pneumoniae isolates, which could not be detected in the disc diffusion method and E-test. Colistin heteroresistance may cause colistin treatment failure in part and may evolve into resistance. Thus, development of more reliable diagnostic methods is required to detect colistin heteroresistance.

Agromyces laixinhei sp. nov. isolated from bat feces in China: Yanpeng Cheng , Yibo Bai , Yuyuan Huang , Jing Yang , Shan Lu , Dong Jin , Ji Pu , Han Zheng , Junqin Li , Ying Huang , Suping Wang , Jianguo Xu; J. Microbiol. 2021;59(5):467-475. Published online March 29, 2021; DOI: https://doi.org/10.1007/s12275-021-0546-5

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Abstract: Three rod-shaped, Gram-stain-positive, and catalase-positive, phenotypically closely related isolates (HY052T, HY050, and HY045) were obtained from fecal samples collected from bats in Guangxi province and Chongqing city of China. Circular, smooth, light-yellow colonies appeared on brain heart infusion plate after 24–48 h incubation at 28°C. The optimal pH for growth was between 6.0 and 7.5. Based on 16S rRNA, the three isolates were phylogenetically related to Agromyces terreus DS-10T, Agromyces aureus AR33T, Agromyces salentinus 20-5T, Agromyces allii UMS-62T, Agromyces lapidis CD55T, and Agromyces italicus CD1T. Moreover, based on 296 core genes, the phylogenomic tree indicated that the three isolates clustered together, closest to Agromyces cerinus VKM Ac- 1340T and Agromyces fucosus VKM Ac-1345T but separated distantly from other Agromyces species. The average nucleotide identity values between strain HY052T and other Agromyces species ranged from 79.3% to 87.9%, lower than the 95–96% threshold. Furthermore, the genome of strain HY052T contains a circular chromosome of 3,437,203 bp with G + C content of 69.0 mol%. Main fatty acids were anteiso-C15:0 and anteiso-C17:0. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, and unidentified glycolipids. Rhamnose, ribose, and glucose were the primary cell wall sugars. The major peptidoglycan amino acids included alanine, glutamic acid, glycine, and 2,4-diaminobutyric acid. An additional remarkable difference from other Agromyces species is that MK-12 was the sole menaquinone in strain HY052T. Based on results from the polyphasic characterizations performed in this study, our isolates are proposed to be members of a novel species in genus Agromyces, named Agromyces laixinhei. The type strain is HY052T (= CGMCC 1.17175T = JCM 33695T).

Diversity and composition of microbiota during fermentation of traditional Nuodeng ham: Xiao-mei Zhang , Xi-jun Dang , Yuan-bing Wang , Tao Sun , Yao Wang , Hong Yu , Wu-song Yang; J. Microbiol. 2021;59(1):20-28. Published online December 23, 2020; DOI: https://doi.org/10.1007/s12275-021-0219-4

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Abstract: The microbial community is one of the most important factors in shaping the characteristics of fermented food. Nuodeng ham, traditionally produced and subjected to 1–4 years of fermentation, is a dry fermented food product with cultural and economic significance to locals in southwestern China. In this study, we aimed to characterize the microbiota and physicochemical profiles of Nuodeng ham across different stages of fermentation. Ham samples from each of the four years were analyzed by sequencing bacterial 16S rRNA gene and fungal internal transcribed spacer sequence, in order to characterize the diversity and composition of their microflora. A total of 2,679,483 bacterial and 2,983,234 fungal sequences of high quality were obtained and assigned to 514 and 57 genera, respectively. Among these microbes, Staphylococcus and Candida were the most abundant genera observed in the ham samples, though samples from different years showed differences in their microbial abundance. Results of physicochemical properties (pH, water, amino acid, NaCl, nitrate and nitrite contents, and the composition of volatile compounds) revealed differences among the ham samples in the composition of volatile compounds, especially in the third year samples, in which no nitrite was detected. These results suggest that the structure and diversity of microbial communities significantly differed across different stages of fermentation. Moreover, the third year hams exhibits a unique and balanced microbial community, which might contribute to the special flavor in the green and safe food products. Thus, our study lends insights into the production of high quality Nuodeng ham.

Characterization of the effects of terminators and introns on recombinant gene expression in the basidiomycete Ceriporiopsis subvermispora: Dong Xuan Nguyen , Emi Nishisaka , Moriyuki Kawauchi , Takehito Nakazawa , Masahiro Sakamoto , Yoichi Honda; J. Microbiol. 2020;58(12):1037-1045. Published online September 30, 2020; DOI: https://doi.org/10.1007/s12275-020-0213-2

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Abstract: Terminators and introns are vital regulators of gene expression in many eukaryotes; however, the functional importance of these elements for controlling gene expression in Agaricomycetes remains unclear. In this study, the effects of Ceriporiopsis subvermispora terminators and introns on the expression of a recombinant hygromycin B phosphotransferase gene (hph) were characterized. Using a transient transformation system, we proved that a highly active terminator (e.g., the gpd terminator) is required for the efficient expression of the hph gene. Mutational analyses of the C. subvermispora gpd terminator revealed that hph expression was dictated by an A-rich region, which included a putative positioning element, and polyadenylation sites. In contrast, our results indicated that introns are not required for the expression of hph directed by the Csβ1-tub and Csgpd promoters in C. subvermispora. This study provides insights into the functions and cis-element requirements of transcriptional terminators in Agaricomycetes, which may be relevant for designing recombinant genes for this important fungal class.

Evolutionary analysis and protein family classification of chitin deacetylases in Cryptococcus neoformans: Seungsue Lee , Hyun Ah Kang , Seong-il Eyun; J. Microbiol. 2020;58(9):805-811. Published online September 1, 2020; DOI: https://doi.org/10.1007/s12275-020-0288-9

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Abstract: Cryptococcus neoformans is an opportunistic fungal pathogen causing cryptococcal meningoencephalitis. Interestingly, the cell wall of C. neoformans contains chitosan, which is critical for its virulence and persistence in the mammalian host. C. neoformans (H99) has three chitin deacetylases (CDAs), which convert chitin to chitosan. Herein, the classification of the chitin-related protein (CRP) family focused on cryptococcal CDAs was analyzed by phylogenetics, evolutionary pressure (dN/dS), and 3D modeling. A phylogenetic tree of 110 CRPs revealed that they can be divided into two clades, CRP I and II with bootstrap values (> 99%). CRP I clade comprises five groups (Groups 1–5) with a total of 20 genes, while CRP II clade comprises sixteen groups (Groups 6–21) with a total of 90 genes. CRP I comprises only fungal CDAs, including all three C. neoformans CDAs, whereas CRP II comprises diverse CDAs from fungi, bacteria, and amoeba, along with other carbohydrate esterase 4 family proteins. All CDAs have the signal peptide, except those from group 11. Notably, CDAs with the putative O-glycosylation site possess either the glycosylphosphatidylinositol (GPI)-anchor motif for CRP I or the chitin-binding domain (CBD) for CRP II, respectively. This evolutionary conservation strongly indicates that the O-glycosylation modification and the presence of either the GPI-anchor motif or the chitin-binding domain is important for fungal CDAs to function efficiently at the cell surface. This study reveals that C. neoformans CDAs carrying GPI anchors have evolved divergently from fungal and bacterial CDAs, providing new insights into evolution and classification of CRP family.

WasC, a WASP family protein, is involved in cell adhesion and migration through regulation of F-actin polymerization in Dictyostelium: Pyeonghwa Jeon , Taeck Joong Jeon; J. Microbiol. 2020;58(8):696-702. Published online June 10, 2020; DOI: https://doi.org/10.1007/s12275-020-0138-9

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Abstract: The actin cytoskeleton is involved in the regulation of cell morphology and migration. Wiskott-Aldrich Syndrome proteins (WASPs) play an important role in controlling actin polymerization by activating the Arp2/3 complex. The present study investigated the roles of WasC, one of the 3 WASPs in Dictyostelium, in cellular processes. Cells lacking WasC displayed strong cell adhesion and approximately 1.5-fold increase in F-actin levels as compared to the wild-type cells. Loss of wasC caused defects in phagocytosis and decreased the migration speed in chemoattractant-mediated cell migration but did not affect directionality. WasC was localized to the protruding region in migrating cells and, transiently and rapidly translocated to the cell cortex in response to chemoattractant stimulation, in an F-actin dependent manner. Our
results
suggest that WasC is involved in cell adhesion and migration by regulating F-actin polymerization at the leading edge of migrating cells, probably as a negative regulator. The increased strength of adhesion in wasC null cells is likely to decrease the migration speed but not the directionality.

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